There are numerous reasons.
- Product variations have no link between them in many cases, especially for websites that sort products according to strict criterias. I have a deco website specialized in US & Canada deco. I don't want that a poster of New York be in the same product page that one of Miami ! (How customers will easily find it from my city categories ?!). Variations are useful for sizes or colors, not much more.
- Products only in variations are hidden as long as the client doesn't click on the product which picture is displayed (if the first picture is not attractive for a given customer, he won't see product variations which contrary might be attractive for him).
- In google Adwords, it prevents from doing relevant ads with relevant links and landing pages
- It prevents from analyzing the Ads campaigns results in a good way because of a lack of relevant product categories because of products in variations and therefore not organized in relevant categories
- The content of the pages with non relevant variations is unclear for search engines, especially for organic searches
- And so on...